RMBlast is a RepeatMasker-compatible version of the standard NCBI blastn program. RMBlast supports RepeatMasker searches by adding a few necessary features to the stock NCBI blastn program. These include:

• Support for custom matrices ( without KA-Statistics ).
• Support for cross_match-like complexity adjusted scoring. Cross_match is Phil Green's seeded smith-waterman search algorithm.
• Support for cross_match-like masklevel filtering.

• RMBlast Main Site

• Module Name: rmblast (see the modules page for more information)

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ rmblastn
[user@cn3144 ~]$  
[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. rmblast.sh). For example:

#!/bin/sh
set -e
module load rmblast
rmblastn -query query.fasta -subject reference.fasta

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] rmblast.sh

Create a swarmfile (e.g. rmblast.swarm). For example:

rmblastn -query query01.fasta -subject reference.fasta
rmblastn -query query02.fasta -subject reference.fasta
rmblastn -query query03.fasta -subject reference.fasta
rmblastn -query query04.fasta -subject reference.fasta

Submit this job using the swarm command.

swarm -f rmblast.swarm [-g #] [-t #] --module rmblast